This is a bug that Crunchyroll has known for a while and is trying to fix. They recently submitted an update for the app to Apple so once it gets approved we will see if it fixes the problem.

There is a work around for now. When it restarts the video pause the video and take note of the time on the scrubbing bar, then close the app by doing the double clock home button method and clear it from the multitasking bar by pressing the red -. Open the app again and go back to your video. Use the scrubbing bar to then scrub back to a spot right before it restarted the video. IE, if the video started to replay from the beginning at 10:15 then scrub back to say 10:00 minutes into the video.

If you have a new bug or issue that you are unable to fix after reading the iOS thread you can use CR's Contact Us form to report the issue. This is usually the best method for getting help with a problem or getting more information. http://www.crunchyroll.com/help?topic=contact (This can be found at the bottom of every page as well for future reference)